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Bai C, Liu J, Zhang X, Li Y, Qin Q, Song H, Yuan C, Huang Z. Research status and challenges of plant-derived exosome-like nanoparticles. Biomed Pharmacother 2024; 174:116543. [PMID: 38608523 DOI: 10.1016/j.biopha.2024.116543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
In recent years, there has been an increasing number of related studies on exosomes. Most studies have focused on exosomes derived from mammals, confirming the important role that exosomes play in cell communication. Plants, as a natural ingredient, plant-derived exosomes have been confirmed to have similar structures and functions to mammalian-derived exosomes. Plant-derived exosome-like nanoparticles (PELNs) are lipid bilayer membrane nanovesicles containing bioactive constituents such as miRNA, mRNA, protein, and lipids obtained from plant cells, that can participate in intercellular communication and mediate transboundary communication, have high bioavailability and low immunogenicity, are relatively safe, and have been shown to play an important role in maintaining cell homeostasis and preventing, and treating a variety of diseases. In this review, we describe the biogenesis, isolation and purification methods, structural composition, stability, safety, function of PELNs and challenges. The functions of PELNs in anti-inflammatory, antioxidant, antitumor and drug delivery are mainly described, and the status of research on exosome nanoparticles of Chinese herbal medicines is outlined. Overall, we summarized the importance of PELNs and the latest research results in this field and provided a theoretical basis for the future research and clinical application of PELNs.
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Affiliation(s)
- Chunmei Bai
- The Fifth Clinical Medical College of Shanxi Medical University, Xinjian South Road, Yingze District, Taiyuan City, Shanxi Province, 030001, China
| | - Jianrong Liu
- The Fifth Clinical Medical College of Shanxi Medical University, Xinjian South Road, Yingze District, Taiyuan City, Shanxi Province, 030001, China; Department of reproductive medicine of Shanxi Provincial People's Hospital, Shuangtaxi Street, Taiyuan City, 030012, China.
| | - Xumin Zhang
- The Fifth Clinical Medical College of Shanxi Medical University, Xinjian South Road, Yingze District, Taiyuan City, Shanxi Province, 030001, China
| | - Yang Li
- The Fifth Clinical Medical College of Shanxi Medical University, Xinjian South Road, Yingze District, Taiyuan City, Shanxi Province, 030001, China
| | - Qin Qin
- The Fifth Clinical Medical College of Shanxi Medical University, Xinjian South Road, Yingze District, Taiyuan City, Shanxi Province, 030001, China; Department of reproductive medicine of Shanxi Provincial People's Hospital, Shuangtaxi Street, Taiyuan City, 030012, China
| | - Haixia Song
- Department of reproductive medicine of Shanxi Provincial People's Hospital, Shuangtaxi Street, Taiyuan City, 030012, China
| | - Caixia Yuan
- Department of reproductive medicine of Shanxi Provincial People's Hospital, Shuangtaxi Street, Taiyuan City, 030012, China
| | - Ziwei Huang
- Department of reproductive medicine of Shanxi Provincial People's Hospital, Shuangtaxi Street, Taiyuan City, 030012, China
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Kim KR, Park SY, Kim H, Kim J, Hong JM, Kim SY, Yu JN. Genome assembly and microsatellite marker development using Illumina and PacBio sequencing in Persicaria maackiana (Polygonaceae) from Korea. Genes Genomics 2024; 46:187-202. [PMID: 38240922 DOI: 10.1007/s13258-023-01479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/23/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Persicaria maackiana (Regel) is a potential medicinal plant that exerts anti-diabetic effects. However, the lack of genomic information on P. maackiana hinders research at the molecular level. OBJECTIVE Herein, we aimed to construct a draft genome assembly and obtain comprehensive genomic information on P. maackiana using high-throughput sequencing tools PacBio Sequel II and Illumina. METHODS Persicaria maackiana samples from three natural populations in Gaecheon, Gichi, and Uiryeong reservoirs in South Korea were used to generate genomic DNA libraries, perform genome de novo assembly, gene ontology analysis, phylogenetic tree analysis, genotyping, and identify microsatellite markers. RESULTS The assembled P. maackiana genome yielded 32,179 contigs. Assessment of assembly integrity revealed 1503 (93.12%) complete Benchmarking Universal Single-Copy Orthologs. A total of 64,712 protein-coding genes were predicted and annotated successfully in the protein database. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs, 13,778 genes were annotated into 18 categories. Genes that activated AMPK were identified in the KEGG pathway. A total of 316,992 microsatellite loci were identified, and primers targeting the flanking regions were developed for 292,059 microsatellite loci. Of these, 150 primer sets were randomly selected for amplification, and 30 of these primer sets were identified as polymorphic. These primers amplified 3-9 alleles. The mean observed and expected heterozygosity were 0.189 and 0.593, respectively. Polymorphism information content values of the markers were 0.361-0.754. CONCLUSION Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.
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Affiliation(s)
- Kang-Rae Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - So Young Park
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Heesoo Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jiyeon Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jeong Min Hong
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Sun-Yu Kim
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jeong-Nam Yu
- Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea.
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Lv S, Wang Q, Zhang X, Ning F, Liu W, Cui M, Xu Y. Mechanisms of multi-omics and network pharmacology to explain traditional chinese medicine for vascular cognitive impairment: A narrative review. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 123:155231. [PMID: 38007992 DOI: 10.1016/j.phymed.2023.155231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/07/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND The term "vascular cognitive impairment" (VCI) describes various cognitive conditions that include vascular elements. It increases the risk of morbidity and mortality in the elderly population and is the most common cognitive impairment associated with cerebrovascular disease. Understanding the etiology of VCI may aid in identifying approaches to target its possible therapy for the condition. Treatment of VCI has focused on vascular risk factors. There are no authorized conventional therapies available right now. The medications used to treat VCI are solely approved for symptomatic relief and are not intended to prevent or slow the development of VCI. PURPOSE The function of Chinese medicine in treating VCI has not yet been thoroughly examined. This review evaluates the preclinical and limited clinical evidence to comprehend the "multi-component, multi-target, multi-pathway" mechanism of Traditional Chinese medicine (TCM). It investigates the various multi-omics approaches in the search for the pathological mechanisms of VCI, as well as the new research strategies, in the hopes of supplying supportive evidence for the clinical treatment of VCI. METHODS This review used the Preferred Reporting Items for Preferred reporting items for systematic reviews and meta-analyses (PRISMA) statements. Using integrated bioinformatics and network pharmacology approaches, a thorough evaluation and analysis of 25 preclinical studies published up to July 1, 2023, were conducted to shed light on the mechanisms of TCM for vascular cognitive impairment. The studies for the systematic review were located using the following databases: PubMed, Web of Science, Scopus, Cochrane, and ScienceDirect. RESULTS We discovered that the multi-omics analysis approach would hasten the discovery of the role of TCM in the treatment of VCI. It will explore components, compounds, targets, and pathways, slowing the progression of VCI from the perspective of inhibiting oxidative stress, stifling neuroinflammation, increasing cerebral blood flow, and inhibiting iron deposition by a variety of molecular mechanisms, which have significant implications for the treatment of VCI. CONCLUSION TCM is a valuable tool for developing dementia therapies, and further research is needed to determine how TCM components may affect the operation of the neurovascular unit. There are still some limitations, although several research have offered invaluable resources for searching for possible anti-dementia medicines and treatments. To gain new insights into the molecular mechanisms that precisely modulate the key molecules at different levels during pharmacological interventions-a prerequisite for comprehending the mechanism of action and determining the potential therapeutic value of the drugs-further research should employ more standardized experimental methods as well as more sophisticated science and technology. Given the results of this review, we advocate integrating chemical and biological component analysis approaches in future research on VCI to provide a more full and objective assessment of the standard of TCM. With the help of bioinformatics, a multi-omics analysis approach will hasten the discovery of the role of TCM in the treatment of VCI, which has significant implications for the treatment of VCI.
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Affiliation(s)
- Shi Lv
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Qian Wang
- Department of Central Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian 271000, China
| | - Xinlei Zhang
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Fangli Ning
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Wenxin Liu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Mengmeng Cui
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China.
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Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2023:elad050. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
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Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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Li ZF, Feng JK, Zhao XC, Liu W, Gu SA, Li R, Lu YL, Mao RJ, Xia LL, Dong LL, Zhang LW, Ruan JY, Liu J, Li GF, Li T, Sun R, Qiu SL, Zheng ZZ, Dong T. The Extract of Pinellia Ternata-Induced Apoptosis of Leukemia Cells by Regulating the Expression of Bax, Bcl-2 and Caspase-3 Protein Expression in Mice. Transplant Proc 2023; 55:2232-2240. [PMID: 37777366 DOI: 10.1016/j.transproceed.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/17/2023] [Accepted: 08/01/2023] [Indexed: 10/02/2023]
Abstract
The study aims to lessen the monetary burden on patients and society by decreasing the price of proprietary drugs used in leukemia therapy. Flow cytometry, reverse transcription polymerase chain reaction, western blot, and a patient-derived xenograft mouse model were used to confirm the therapeutic effect of Pinellia ternata extract on leukemia. Three types of leukemia cells (K562, HL-60, and C8166 cell lines) were found to undergo early apoptosis (P ≤ .05) after being exposed to P. ternata extract, as measured by flow cytometry. Reverse transcription polymerase chain reaction results showed that P. ternata extract at both middle (300 μg/mL) and high (500 μg/mL) concentrations was able to down-regulate Bcl-2 and upregulate mRNA expression of Bax and caspase-3. In the patient-derived xenograft mouse model formed by BALB/c-nu/nu nude mice, immunohistochemistry indicated that P. ternata extract effectively suppressed the proliferation of leukemia cells. Therefore, P. ternata extract at 300 μg/mL and 500 μg/mL could effectively inhibit myeloid and lymphocytic leukemia cell proliferation and promote leukemia cell apoptosis by regulating Bax/Bcl-2 and caspase-3.
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Affiliation(s)
- Zheng-Fa Li
- Department of Hematology, Department of Laboratory of the First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, Yunnan, China
| | - Jia-Kun Feng
- Department of Hematology, Department of Laboratory of the First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, Yunnan, China
| | - Xiao-Chen Zhao
- Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Wei Liu
- Department of Hematology, Department of Laboratory of the First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, Yunnan, China
| | - Shi-An Gu
- Department of Hematology, Department of Laboratory of the First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, Yunnan, China
| | - Rui Li
- Department of Hematology, Department of Laboratory of the First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, Yunnan, China
| | - Yang-Liu Lu
- Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Rui-Jiao Mao
- Department of Hematology, Department of Laboratory of the First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, Yunnan, China
| | - Li-Ling Xia
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Lu-Lu Dong
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Li-Wen Zhang
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Jing-Yan Ruan
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Jiao Liu
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Guang-Fen Li
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Tao Li
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Rong Sun
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | - Shui-Lan Qiu
- Department of Hematology, Department of Pathology of Yunnan New Kun Hua Hospital, Kunming, Yunnan, China
| | | | - Ting Dong
- Department of Hematology, Department of Laboratory of the First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, Yunnan, China.
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Huang X, Gao L, Deng R, Peng Y, Wu S, Lu J, Liu X. Huangqi-Danshen decoction reshapes renal glucose metabolism profiles that delays chronic kidney disease progression. Biomed Pharmacother 2023; 164:114989. [PMID: 37315436 DOI: 10.1016/j.biopha.2023.114989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Abstract
Huangqi-Danshen decoction (HDD), a Chinese herbal preparation, is effective in clinical treatment of chronic kidney disease (CKD). However, the underlying mechanism remains to be clarified. In this study, we aimed to investigate the role of HDD in the regulation of renal glucose metabolism in a CKD mouse model. The 0.2% adenine-induced CKD mouse model was administered HDD extract at a dose of 6.8 g/kg/day for 4 weeks. Detection of renal glucose metabolites was performed by ultra-performance liquid chromatography-tandem mass spectrometry. The expression of renal fibrosis and glucose metabolism-related proteins was tested by Western blotting, immunohistochemistry, and immunofluorescence. The results showed that HDD treatment could significantly reduce serum creatinine (0.36 ± 0.10 mg/dL vs. 0.51 ± 0.07 mg/dL, P < 0.05) and blood urea nitrogen (40.02 ± 3.73 mg/dL vs. 62.91 ± 10 mg/dL, P < 0.001) levels, and improve renal pathological injury and fibrosis. Aberrant glucose metabolism was found in the kidneys of CKD mice, manifested by enhanced glycolysis and pentose phosphate pathway, and tricarboxylic acid cycle inhibition, which could be partially restored by HDD treatment. Furthermore, HDD regulated the expression of hexokinase 2, phosphofructokinase, pyruvate kinase M2, pyruvate dehydrogenase E1, oxoglutarate dehydrogenase, and glucose-6-phosphate dehydrogenase in CKD mice. In conclusion, HDD protected against adenine-induced CKD, reshaped glucose metabolism profiles, and restored the expression of key enzymes of glucose metabolism in the kidneys of CKD mice. This study sheds light on targeting glucose metabolism for the treatment of CKD and screening small molecule compounds from herbal medicine to slow CKD progression.
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Affiliation(s)
- Xi Huang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China; The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China
| | - Liwen Gao
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China; The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China
| | - Ruyu Deng
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China; Shenzhen Traditional Chinese Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Shenzhen, Guangdong 518033, China
| | - Yu Peng
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China; The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China
| | - Shanshan Wu
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China; The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China
| | - Jiandong Lu
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China
| | - Xinhui Liu
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, China.
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Gao L, Xu W, Xin T, Song J. Application of third-generation sequencing to herbal genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1124536. [PMID: 36959935 PMCID: PMC10027759 DOI: 10.3389/fpls.2023.1124536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants.
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Ma S, Li J, Pei L, Feng N, Zhang Y. Microneedle-based interstitial fluid extraction for drug analysis: Advances, challenges, and prospects. J Pharm Anal 2023; 13:111-126. [PMID: 36908860 PMCID: PMC9999301 DOI: 10.1016/j.jpha.2022.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/28/2022] [Accepted: 12/31/2022] [Indexed: 01/07/2023] Open
Abstract
Similar to blood, interstitial fluid (ISF) contains exogenous drugs and biomarkers and may therefore substitute blood in drug analysis. However, current ISF extraction techniques require bulky instruments and are both time-consuming and complicated, which has inspired the development of viable alternatives such as those relying on skin or tissue puncturing with microneedles. Currently, microneedles are widely employed for transdermal drug delivery and have been successfully used for ISF extraction by different mechanisms to facilitate subsequent analysis. The integration of microneedles with sensors enables in situ ISF analysis and specific compound monitoring, while the integration of monitoring and delivery functions in wearable devices allows real-time dose modification. Herein, we review the progress in drug analysis based on microneedle-assisted ISF extraction and discuss the related future opportunities and challenges.
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Affiliation(s)
- Shuwen Ma
- Department of Pharmaceutical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jiaqi Li
- Department of Pharmaceutical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Lixia Pei
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Nianping Feng
- Department of Pharmaceutical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yongtai Zhang
- Department of Pharmaceutical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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10
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Xie Y, Yang G, Zhang C, Zhang X, Jiang X. Comparative analysis of chloroplast genomes of endangered heterostylous species Primula wilsonii and its closely related species. Ecol Evol 2023; 13:e9730. [PMID: 36694549 PMCID: PMC9842877 DOI: 10.1002/ece3.9730] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/10/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023] Open
Abstract
Primula, well known for its heterostyly, is the largest genus in the family Primulaceae with more than 500 species. The considerable species number has introduced a huge challenge for taxonomy. The phylogenetic relationships among Primula still maintain unresolved due to frequent hybridization and introgression between closely related species. In this study, we sequenced and assembled the complete chloroplast genomes of Primula wilsonii Dunn, which is a PSESP (plant species with extremely small populations), using Illumina sequencing and compared its genomic sequences with those of four related Primula species. The chloroplast genomes of Primula species were similar in the basic structure, gene order, and GC content. The detected 38 SSRs (simple sequence repeats) loci and 17 hypervariable regions had many similarities in P. wilsonii, P. anisodora, P. miyabeana, and P. poissonii, but showed a significant difference compared with those in P. secundiflora. Slight variations were observed among Primula chloroplast genomes, in consideration of the relatively stable patterns of IR (inverted repeats) contraction and expansion. Phylogenetic analysis based on chloroplast genomes and protein-coding genes confirmed three major clades in Chinese Primula, but the infrageneric sections were not in accordance with morphological traits. The P. poissonii complex was confirmed here and P. anisodora was the most closely related species to P. wilsonii. Overall, the chloroplast genome sequences provided useful genetic and evolutionary information for phylogeny and population genetics on Chinese Primula species.
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Affiliation(s)
- YanPing Xie
- School of Life SciencesHuaibei Normal UniversityHuaibeiChina
| | - GangGang Yang
- School of Life SciencesHenan Normal UniversityXinxiangChina
| | - Chan Zhang
- School of Life SciencesHenan Normal UniversityXinxiangChina
| | - XingWang Zhang
- School of Life SciencesHuaibei Normal UniversityHuaibeiChina
| | - XianFeng Jiang
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunmingChina
- College of Agriculture and BioscienceDali UniversityDaliChina
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11
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Zhu X, Yao Q, Yang P, Zhao D, Yang R, Bai H, Ning K. Multi-omics approaches for in-depth understanding of therapeutic mechanism for Traditional Chinese Medicine. Front Pharmacol 2022; 13:1031051. [PMID: 36506559 PMCID: PMC9732109 DOI: 10.3389/fphar.2022.1031051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022] Open
Abstract
Traditional Chinese Medicine (TCM) is extensively utilized in clinical practice due to its therapeutic and preventative treatments for various diseases. With the development of high-throughput sequencing and systems biology, TCM research was transformed from traditional experiment-based approaches to a combination of experiment-based and omics-based approaches. Numerous academics have explored the therapeutic mechanism of TCM formula by omics approaches, shifting TCM research from the "one-target, one-drug" to "multi-targets, multi-components" paradigm, which has greatly boosted the digitalization and internationalization of TCM. In this review, we concentrated on multi-omics approaches in principles and applications to gain a better understanding of TCM formulas against various diseases from several aspects. We first summarized frequently used TCM quality assessment methods, and suggested that incorporating both chemical and biological ingredients analytical methods could lead to a more comprehensive assessment of TCM. Secondly, we emphasized the significance of multi-omics approaches in deciphering the therapeutic mechanism of TCM formulas. Thirdly, we focused on TCM network analysis, which plays a vital role in TCM-diseases interaction, and serves for new drug discovery. Finally, as an essential source for storing multi-omics data, we evaluated and compared several TCM databases in terms of completeness and reliability. In summary, multi-omics approaches have infiltrated many aspects of TCM research. With the accumulation of omics data and data-mining resources, deeper understandings of the therapeutic mechanism of TCM have been acquired or will be gained in the future.
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Affiliation(s)
- Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Yao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Zhao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ronghua Yang
- Dovetree Synbio Company Limited, Shenyang, China,*Correspondence: Ronghua Yang, ; Hong Bai, ; Kang Ning,
| | - Hong Bai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,*Correspondence: Ronghua Yang, ; Hong Bai, ; Kang Ning,
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,*Correspondence: Ronghua Yang, ; Hong Bai, ; Kang Ning,
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Xin T, Li R, Lou Q, Lin Y, Liao H, Sun W, Guan M, Zhou J, Song J. Application of DNA barcoding to the entire traditional Chinese medicine industrial chain: A case study of Rhei Radix et Rhizoma. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 105:154375. [PMID: 35952576 DOI: 10.1016/j.phymed.2022.154375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/20/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Safety concerns, caused by complex and unpredictable adulterants, run through the entire industrial chain of traditional Chinese medicines (TCMs). However, the conventional circulation traceability system only focuses on a certain end or link at the back end of the TCM industrial chain, ignoring the integrity of the links cross the entire industrial chain and lacking traceability. In consequence, a strict and rational supervision system is urgently required for the entire industrial chain. HYPOTHESIS/PURPOSE We hypothesize that DNA barcoding would be a suitable measure for the traceability of adulterants in the entire TCM industrial chain. METHODS In this study, Rhei Radix et Rhizoma was selected as a model to establish a traceability system for the entire TCM industrial chain. A total of 110 samples, including leaves, seeds, roots, decoction pieces, and traditional Chinese patent medicines (TCPMs), were collected upstream, midstream, and downstream of the entire industrial chain of Rhei Radix et Rhizoma. The ndhF-rpl32 fragment rather than the universal DNA barcodes, which could not distinguish the three original species of Rhei Radix et Rhizoma, was selected as a specific DNA barcode to evaluate the practical application of DNA barcoding in the chain. RESULTS The results showed that the ndhF-rpl32 fragment in all samples could be amplified and bi-directionally sequenced. Based on the standard operating procedures of DNA barcoding, the ndhF-rpl32 fragment clearly distinguished the seven Rheum species collected upstream of the entire industrial chain. For the samples collected midstream and downstream of the entire industrial chain, 25% of the 36 commercial decoction pieces samples were identified as adulterants, whereas the eight TCPM samples were all derived from genuine Rhei Radix et Rhizoma. CONCLUSIONS This study shows that DNA barcoding is a powerful and suitable technology that can be applied to trace TCMs in the entire industrial chain, thereby assuring clinical medication safety.
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Affiliation(s)
- Tianyi Xin
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Ranjun Li
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; School of Life and Science, Southwest Jiaotong University, Chengdu 610031, China
| | - Qian Lou
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yulin Lin
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hai Liao
- School of Life and Science, Southwest Jiaotong University, Chengdu 610031, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Meng Guan
- Sinopharm Traditional Chinese Medicine Co., Ltd., Beijing 100097, China
| | - Jiayu Zhou
- School of Life and Science, Southwest Jiaotong University, Chengdu 610031, China
| | - Jingyuan Song
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong 666100, China.
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13
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Hao L, Xu W, Qi G, Xin T, Xu Z, Lei H, Song J. GAGE is a method for identification of plant species based on whole genome analysis and genome editing. Commun Biol 2022; 5:947. [PMID: 36088518 PMCID: PMC9464240 DOI: 10.1038/s42003-022-03894-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Whole genomes of plants should be ideal databases for their species identification, but unfortunately there was no such method before this exploration. Here we report a plant species identification method based on the whole Genome Analysis and Genome Editing (GAGE). GAGE searches for target sequences from the whole genome of the subject plant and specifically detects them by employing a CRISPR/Cas12a system. Similar to how Mendel chose Pisum sativum (pea), we selected Crocus sativus (saffron) to establish GAGE, in which we constructed a library containing all candidate target sequences. Taking a target sequence in the ITS2 region as an example, we confirmed the feasibility, specificity, and sensitivity of GAGE. Consequently, we succeeded in not only using GAGE to identify Cr. sativus and its adulterants, but also executing GAGE in the plants from different classes including angiosperms, gymnosperms, ferns, and lycophytes. This sensitive and rapid method is the first plant species identification method based on the whole genome and provides new insights into the application of the whole genome in species identification. A plant species identification method, GAGE, is reported that searches for target sequences from the whole genome of the subject plant and specifically detects them by employing a CRISPR/Cas12a system.
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Zhang S, Rao S, Yang MW, Huang YT, Hong FF, Yang SL. Pharmacological effects of the Cassia Seed on atherosclerosis: A meta-analysis based on network pharmacology. Medicine (Baltimore) 2022; 101:e30411. [PMID: 36086754 PMCID: PMC10980403 DOI: 10.1097/md.0000000000030411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 07/26/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The aim of this study was to shed light on the active ingredients and potential targets of Cassia Seed about anti-atherosclerosis based on network pharmacology. METHODS The active ingredients and potential targets of Cassia Seed were obtained from traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) and SwissTargetPrediction database. Then, atherosclerosis-related targets were screened via GeneCards, online mendelian inheritance in man, therapeutic target database and DrugBank database. The common targets and protein-protein interaction (PPI) network was later identified and built. Furthermore, we used the database for annotation, visualization and integrated discovery (DAVID) database server to accomplish the enrichment analysis. The compounds-targets-pathways network was ultimately constructed by Cytoscape. RESULTS A total of 14 active ingredients and 475 related targets were sifted from Cassia Seed. Among 574 potential atherosclerotic targets, there were 99 targets overlapped with those of Cassia Seed. Topological analysis with Cytoscape revealed that proto-oncogene tyrosine-protein kinase proto-oncogene tyrosine-protein kinase Src, transcription factor AP-1 (JUN), mitogen-activated protein kinase 8 (MAPK8), mitogen-activated protein kinase 14 (MAPK14) and catenin beta-1 were considered as the hub gene. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis suggested that the Cassia Seed had the potential to influence varieties of biological processes and pathways, including positive regulation of smooth muscle cell proliferation, inflammatory response, tumor necrosis factor (TNF) signaling pathway, vascular endothelial growth factor (VEGF) signaling pathway and arachidonic acid (ARA) metabolism. CONCLUSION Taken together, our findings support that anti-atherosclerosis effects of Cassia Seed are characterized by multi-component, multi-target and multi-path mechanism of action.
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Affiliation(s)
- Sen Zhang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang, China
| | - Sijing Rao
- Department of Physiology, College of Medicine, Nanchang University, Nanchang, China
| | - Mei Wen Yang
- Department of Surgery, Fuzhou Medical College, Nanchang University, Jiangxi, Fuzhou, China
| | - Ya-Ting Huang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang, China
| | - Fen-Fang Hong
- Experimental Center of Pathogen Biology, Nanchang University, Nanchang, China
| | - Shu-Long Yang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang, China
- Key Research Laboratory of Chronic Diseases, Fuzhou Medical College, Nanchang University, Fuzhou, China
- Department of Physiology, Fuzhou Medical College, Nanchang University, Jiangxi, Fuzhou, China
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15
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Gao ZR, Feng YZ, Zhao YQ, Zhao J, Zhou YH, Ye Q, Chen Y, Tan L, Zhang SH, Feng Y, Hu J, Ou-Yang ZY, Dusenge MA, Guo Y. Traditional Chinese medicine promotes bone regeneration in bone tissue engineering. Chin Med 2022; 17:86. [PMID: 35858928 PMCID: PMC9297608 DOI: 10.1186/s13020-022-00640-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/30/2022] [Indexed: 11/10/2022] Open
Abstract
Bone tissue engineering (BTE) is a promising method for the repair of difficult-to-heal bone tissue damage by providing three-dimensional structures for cell attachment, proliferation, and differentiation. Traditional Chinese medicine (TCM) has been introduced as an effective global medical program by the World Health Organization, comprising intricate components, and promoting bone regeneration by regulating multiple mechanisms and targets. This study outlines the potential therapeutic capabilities of TCM combined with BTE in bone regeneration. The effective active components promoting bone regeneration can be generally divided into flavonoids, alkaloids, glycosides, terpenoids, and polyphenols, among others. The chemical structures of the monomers, their sources, efficacy, and mechanisms are described. We summarize the use of compounds and medicinal parts of TCM to stimulate bone regeneration. Finally, the limitations and prospects of applying TCM in BTE are introduced, providing a direction for further development of novel and potential TCM.
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Affiliation(s)
- Zheng-Rong Gao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Yun-Zhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Ya-Qiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Jie Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Ying-Hui Zhou
- Department of Endocrinology and Metabolism, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, National Clinical Research Center for Metabolic Disease, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qin Ye
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Yun Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Li Tan
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Shao-Hui Zhang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Yao Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Jing Hu
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Ze-Yue Ou-Yang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Marie Aimee Dusenge
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha, 410011, Hunan, China.
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Xu Z, Li Z, Ren F, Gao R, Wang Z, Zhang J, Zhao T, Ma X, Pu X, Xin T, Rombauts S, Sun W, Van de Peer Y, Chen S, Song J. The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:217-230. [PMID: 35476217 PMCID: PMC7614287 DOI: 10.1111/tpj.15788] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/05/2022] [Accepted: 04/24/2022] [Indexed: 05/05/2023]
Abstract
Species belonging to the order Ranunculales have attracted much attention because of their phylogenetic position as a sister group to all other eudicot lineages and their ability to produce unique yet diverse benzylisoquinoline alkaloids (BIAs). The Papaveraceae family in Ranunculales is often used as a model system for studying BIA biosynthesis. Here, we report the chromosome-level genome assembly of Corydalis tomentella, a species of Fumarioideae, one of the two subfamilies of Papaveraceae. Based on comparisons of sequenced Ranunculalean species, we present clear evidence of a shared whole-genome duplication (WGD) event that has occurred before the divergence of Ranunculales but after its divergence from other eudicot lineages. The C. tomentella genome enabled us to integrate isotopic labeling and comparative genomics to reconstruct the BIA biosynthetic pathway for both sanguinarine biosynthesis shared by papaveraceous species and the cavidine biosynthesis that is specific to Corydalis. Also, our comparative analysis revealed that gene duplications, especially tandem gene duplications, underlie the diversification of BIA biosynthetic pathways in Ranunculales. In particular, tandemly duplicated berberine bridge enzyme-like genes appear to be involved in cavidine biosynthesis. In conclusion, our study of the C. tomentella genome provides important insights into the occurrence of WGDs during the early evolution of eudicots, as well as into the evolution of BIA biosynthesis in Ranunculales.
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Affiliation(s)
- Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Fengming Ren
- Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, China
| | - Ranran Gao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Zhe Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinlan Zhang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- Academy for Advanced Interdisciplinary Studies and College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Corresponding Authors: Jingyuan Song (), Shilin Chen (), and Yves Van de Peer ()
| | - Shilin Chen
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
- Corresponding Authors: Jingyuan Song (), Shilin Chen (), and Yves Van de Peer ()
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong 666100, China
- Corresponding Authors: Jingyuan Song (), Shilin Chen (), and Yves Van de Peer ()
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17
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Lou Q, Xin T, Xu W, Li R, Song J. TaqMan Probe-Based Quantitative Real-Time PCR to Detect Panax notoginseng in Traditional Chinese Patent Medicines. Front Pharmacol 2022; 13:828948. [PMID: 35685641 PMCID: PMC9171072 DOI: 10.3389/fphar.2022.828948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background: There has been global concern about the safety and accuracy of traditional Chinese patent medicines (TCPMs). Panax notoginseng, also known as sanqi, is an important constituent of TCPMs. However, identifying the species contained in TCPMs is challenging due to the presence of multiple ingredients and the use of various preparation processes.Objective: To detect P. notoginseng in TCPMs.Methods: A TaqMan probe-based qPCR assay was constructed and validated with DNA extracted from P. notoginseng and adulterants. In total, 75 samples derived from 25 batches of TCPMs were tested using the constructed qPCR method.Results: A TaqMan probe-based qPCR assay targeting P. notoginseng was established. The constructed qPCR assay could specifically discriminate P. notoginseng from Panax ginseng, Panax quinquefolium and Curcuma aromatica Salisb. cv. Wenyujin. The sensitivity study showed that the detectable DNA template concentration of P. notoginseng for this qPCR assay was 0.001 ng/μl. All 75 samples from TCPMs were confirmed to contain P. notoginseng by the qPCR assay.Conclusions: The qPCR method can accurately identify P. notoginseng in TCPMs and is promising as a powerful tool for quality control and market regulation.
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Affiliation(s)
- Qian Lou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenjie Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ranjun Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, China
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18
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Xu Q, Niu SC, Li KL, Zheng PJ, Zhang XJ, Jia Y, Liu Y, Niu YX, Yu LH, Chen DF, Zhang GQ. Chromosome-Scale Assembly of the Dendrobium nobile Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of Dendrobium. Front Genet 2022; 13:844622. [PMID: 35299950 PMCID: PMC8921531 DOI: 10.3389/fgene.2022.844622] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 01/07/2023] Open
Abstract
Orchids constitute approximately 10% of flowering plant species. However, only about 10 orchid genomes have been published. Metabolites are the main way through which orchids respond to their environment. Dendrobium nobile, belonging to Dendrobium, the second largest genus in Orchidaceae, has high ornamental, medicinal, and ecological value. D. nobile is the source of many popular horticultural varieties. Among the Dendrobium species, D. nobile has the highest amount of dendrobine, which is regarded as one of the criteria for evaluating medicinal quality. Due to lack of data and analysis at the genomic level, the biosynthesis pathways of dendrobine and other related medicinal ingredients in D. nobile are unknown. In this paper, we report a chromosome-scale reference genome of D. nobile to facilitate the investigation of its genomic characteristics for comparison with other Dendrobium species. The assembled genome size of D. nobile was 1.19 Gb. Of the sequences, 99.45% were anchored to 19 chromosomes. Furthermore, we identified differences in gene number and gene expression patterns compared with two other Dendrobium species by integrating whole-genome sequencing and transcriptomic analysis [e.g., genes in the polysaccharide biosynthesis pathway and upstream of the alkaloid (dendrobine) biosynthesis pathway]. Differences in the TPS and CYP450 gene families were also found among orchid species. All the above differences might contribute to the species-specific medicinal ingredient biosynthesis pathways. The metabolic pathway-related analysis will provide further insight into orchid responses to the environment. Additionally, the reference genome will provide important insights for further molecular elucidation of the medicinal active ingredients of Dendrobium and enhance the understanding of orchid evolution.
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Affiliation(s)
- Qing Xu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
| | - Shan-Ce Niu
- College of Horticulture, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Kang-Li Li
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Pei-Ji Zheng
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Jing Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yin Jia
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yang Liu
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yun-Xia Niu
- School of Vocational Education, Tianjin University of Technology and Education, Tianjin, China
| | - Li-Hong Yu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Duan-Fen Chen
- College of Horticulture, Hebei Agricultural University, Baoding, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
| | - Guo-Qiang Zhang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
- Laboratory for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, The National Orchid Conservation Center of China, Shenzhen, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
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Li DD, Yu P, Xiao W, Wang ZZ, Zhao LG. Berberine: A Promising Natural Isoquinoline Alkaloid for the Development of Hypolipidemic Drugs. Curr Top Med Chem 2021; 20:2634-2647. [PMID: 32901585 DOI: 10.2174/1568026620666200908165913] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 05/28/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022]
Abstract
Berberine, as a representative isoquinoline alkaloid, exhibits significant hypolipidemic activity in both animal models and clinical trials. Recently, a large number of studies on the lipid-lowering mechanism of berberine and studies for improving its hypolipidemic activity have been reported, but for the most part, they have been either incomplete or not comprehensive. In addition, there have been a few specific reviews on the lipid-reducing effect of berberine. In this paper, the physicochemical properties, the lipid-lowering mechanism, and studies of the modification of berberine all are discussed to promote the development of berberine as a lipid-lowering agent. Subsequently, this paper provides some insights into the deficiencies of berberine in the study of lipid-lowering drug, and based on the situation, some proposals are put forward.
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Affiliation(s)
- Dong-Dong Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China,College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Pan Yu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China,College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Wei Xiao
- Jiangsu Kanion Pharmaceutical Co., Ltd., 58 Haichang South Road, Lianyungang 222001, China
| | - Zhen-Zhong Wang
- Jiangsu Kanion Pharmaceutical Co., Ltd., 58 Haichang South Road, Lianyungang 222001, China
| | - Lin-Guo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China,College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
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20
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Ren F, Wang L, Li Y, Zhuo W, Xu Z, Guo H, Liu Y, Gao R, Song J. Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola. Ecol Evol 2021; 11:4158-4171. [PMID: 33976800 PMCID: PMC8093665 DOI: 10.1002/ece3.7312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/27/2023] Open
Abstract
The increasingly wide application of chloroplast (cp) genome super-barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus Corydalis. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and Corydalis tomentella in Corydalis, conducted a comparison of these cp genomes among each other as well as with others of Papaveraceae. The cp genomes have a large genome size of 189,029-190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955-42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola, and Papaveraceae species, five NADH dehydrogenase-like genes (ndhF, ndhD, ndhL, ndhG, and ndhE) with psaC, rpl32, ccsA, and trnL-UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU, and trnL-CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.
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Affiliation(s)
- Fengming Ren
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | | | - Ying Li
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
| | - Wei Zhuo
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | - Zhichao Xu
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
| | | | - Yan Liu
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | - Ranran Gao
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
| | - Jingyuan Song
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
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21
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Hao L, Pu X, Song J. Introduction of mutations in plants with prime editing. Methods 2021; 194:83-93. [PMID: 33774158 DOI: 10.1016/j.ymeth.2021.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/26/2022] Open
Abstract
The emergence of a clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas) system has had a revolutionary impact on plant biology. However, this system and further developed base editing are limited by their inherent imperfection. Prime editing, a just arrival technology based on CRISPR/Cas, can directly and precisely edit a specified DNA site without double strand breaks and donor DNA by integrating an engineered reverse transcriptase (RT) with a catalytically impaired Cas9 endonuclease and introducing genetic information into prime editing guide RNA (pegRNA). In addition, it has a wider range of editing types than base editing and can install all types of editing theoretically. Prime editing was originally developed in mammalian cells and has recently been applied to plants. Here, we describe the origin of prime editing and compare it with traditional CRISPR/Cas9 and base editing; then, we exemplify it in plants, including strategies and methods. Accordingly, we generate the overall procedures of prime editing to provide instructions for its application. Furthermore, we summarize its improvements in the approach, such as optimizing the length of a primer binding site and RT template, as well as pursuing an optimal nicking site in the unedited sequence. Finally, we discuss the potential impact on domestication and improvement of agricultural crops, sustainable utilization of medicinal plants, cultivation of varieties of horticultural plants, and revelation of the genetic code, in order to offer a reference for the further study and development of prime editing.
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Affiliation(s)
- Lijun Hao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, 151 Malianwa North Road, Haidian District, Beijing 100193, China.
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22
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Xu Z, Gao R, Pu X, Xu R, Wang J, Zheng S, Zeng Y, Chen J, He C, Song J. Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:230-240. [PMID: 33157301 PMCID: PMC7801248 DOI: 10.1016/j.gpb.2020.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/20/2020] [Accepted: 06/12/2020] [Indexed: 01/06/2023]
Abstract
Scutellaria baicalensis (S. baicalensis) and Scutellaria barbata (S. barbata) are common medicinal plants of the Lamiaceae family. Both produce specific flavonoid compounds, including baicalein, scutellarein, norwogonin, and wogonin, as well as their glycosides, which exhibit antioxidant and antitumor activities. Here, we report chromosome-level genome assemblies of S. baicalensis and S. barbata with quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred far earlier than previously reported, and a whole-genome duplication (WGD) event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. Comparative genome analysis of the congeneric species revealed the species-specific evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplication of genes encoding phenylalanine ammonia lyase and chalcone synthase, and the S. barbata-specific duplication of genes encoding 4-CoA ligase. In addition, the paralogous duplication, colinearity, and expression diversity of CYP82D subfamily members revealed the functional divergence of genes encoding flavone hydroxylase between S. baicalensis and S. barbata. Analyzing these Scutellaria genomes reveals the common and species-specific evolution of flavone biosynthetic genes. Thus, these findings would facilitate the development of molecular breeding and studies of biosynthesis and regulation of bioactive compounds.
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Affiliation(s)
- Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Ranran Gao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Rong Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Jiyong Wang
- China National Traditional Chinese Medicine Co., Ltd, Beijing 102600, China
| | - Sihao Zheng
- China National Traditional Chinese Medicine Co., Ltd, Beijing 102600, China
| | - Yan Zeng
- China National Traditional Chinese Medicine Co., Ltd, Beijing 102600, China
| | - Jun Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Chunnian He
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China.
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Li L, Jiang Y, Liu Y, Niu Z, Xue Q, Liu W, Ding X. The large single-copy (LSC) region functions as a highly effective and efficient molecular marker for accurate authentication of medicinal Dendrobium species. Acta Pharm Sin B 2020; 10:1989-2001. [PMID: 33163349 PMCID: PMC7606094 DOI: 10.1016/j.apsb.2020.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/19/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Having great medicinal values, Dendrobium species of "Fengdou" (DSFs) are a taxonomically complex group in Dendrobium genus including many closely related and recently diverged species. Traditionally used DNA markers have been proved to be insufficient in authenticating many species of this group. Here, we investigated 101 complete plastomes from 23 DSFs, comprising 72 newly sequenced and 29 documented, which all exhibited well-conserved genomic organization and gene order. Plastome-wide comparison showed the co-occurrence of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), which can be explained by both the repeat-associated and indel-associated mutation hypotheses. Moreover, guanine-cytosine (GC) content was found to be negatively correlated with the three divergence variables (SNPs, indels and repeats), indicating that GC content may reflect the level of the local sequence divergence. Our species authentication analyses revealed that the relaxed filtering strategies of sequence alignment had no negative impact on species identification. By assessing the maximum likelihood (ML) trees inferred from different datasets, we found that the complete plastome and large single-copy (LSC) datasets both successfully identified all 23 DSFs with the maximum bootstrap values. However, owing to the high efficiency of LSC in species identification, we recommend using LSC for accurate authentication of DSFs.
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Affiliation(s)
- Ludan Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yu Jiang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuanyuan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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24
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Pu X, Li Z, Tian Y, Gao R, Hao L, Hu Y, He C, Sun W, Xu M, Peters RJ, Van de Peer Y, Xu Z, Song J. The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration. THE NEW PHYTOLOGIST 2020; 227:930-943. [PMID: 32187685 PMCID: PMC7116227 DOI: 10.1111/nph.16552] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/12/2020] [Indexed: 05/12/2023]
Abstract
Lonicera japonica is a widespread member of the Caprifoliaceae (honeysuckle) family utilized in traditional medical practices. This twining vine honeysuckle also is a much-sought ornamental, in part due to its dynamic flower coloration, which changes from white to gold during development. The molecular mechanism underlying dynamic flower coloration in L. japonica was elucidated by integrating whole genome sequencing, transcriptomic analysis and biochemical assays. Here, we report a chromosome-level genome assembly of L. japonica, comprising nine pseudochromosomes with a total size of 843.2 Mb. We also provide evidence for a whole-genome duplication event in the lineage leading to L. japonica, which occurred after its divergence from Dipsacales and Asterales. Moreover, gene expression analysis not only revealed correlated expression of the relevant biosynthetic genes with carotenoid accumulation, but also suggested a role for carotenoid degradation in L. japonica's dynamic flower coloration. The variation of flower color is consistent with not only the observed carotenoid accumulation pattern, but also with the release of volatile apocarotenoids that presumably serve as pollinator attractants. Beyond novel insights into the evolution and dynamics of flower coloration, the high-quality L. japonica genome sequence also provides a foundation for molecular breeding to improve desired characteristics.
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Affiliation(s)
- Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ya Tian
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Ranran Gao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Lijun Hao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yating Hu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Chunnian He
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Meimei Xu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011-1079, USA
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011-1079, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- Corresponding Authors: Jingyuan Song: , 86-10-57833199; Zhichao Xu: , 86-10-57833199
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong 666100, China
- Corresponding Authors: Jingyuan Song: , 86-10-57833199; Zhichao Xu: , 86-10-57833199
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25
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Zhang JH, Lv HZ, Liu WJ, Ji AJ, Zhang X, Song JY, Luo HM, Chen SL. bHLH transcription factor SmbHLH92 negatively regulates biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza. CHINESE HERBAL MEDICINES 2020; 12:237-246. [PMID: 36119017 PMCID: PMC9476745 DOI: 10.1016/j.chmed.2020.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/25/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
Objective Salvia miltiorrhiza is a valuable herbal medicine with tanshinone and phenolic acid as the main biological active ingredients. The biosynthetic regulation of these bioactive compounds is controlled by a set of transcription factors (TFs). The basic helix-loop-helix (bHLH) transcription factor plays an important role in various physiological and biochemical processes in plants. However, research on bHLH TFs regulating phenolic acid or tanshinone biosynthesis in S. miltiorrhiza is limited. Methods qRT-PCR was used for gene expression analysis. The subcellular localization of SmbHLH92 was detected by SmbHLH92-GFP transient transformation into tobacco leaves, and its fluorescence was observed using a confocal laser scanning microscope. The transcriptional activity of SmbHLH92 was confirmed in the AH109 yeast strain. RNA interference hairy roots of SmbHLH92-RNAi transgenic lines were obtained through Agrobacterium-mediated genetic transformation. Ultra performance liquid chromatography (UPLC) was used to detect the changes of phenolic acids and tanshinones. Results SmbHLH92 is a bHLH transcription factor that is highly expressed in the root and phloem of S. miltiorrhiza. The subcellular localization and transcriptional activity of SmbHLH92 indicated that SmbHLH92 was located in the nucleus and may be a transcription factor. RNA interference (RNAi) of SmbHLH92 in hairy roots of S. miltiorrhiza significantly increased the accumulation of phenolic acid and tanshinone. Quantitative RT-PCR (RT-qPCR) analysis showed the transcription level of genes encoding the key enzymes involved in the phenolic acid and tanshinone biosynthetic pathways was increased in the hairy roots of the SmbHLH92-RNAi transgenic line, comparing with the control line. Conclusion These data indicate that SmbHLH92 is a negative regulator involved in the regulation of phenolic acid and tanshinone biosynthesis in S. miltiorrhiza.
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Pu X, He C, Yang Y, Wang W, Hu K, Xu Z, Song J. In Vivo Production of Five Crocins in the Engineered Escherichia coli. ACS Synth Biol 2020; 9:1160-1168. [PMID: 32216376 DOI: 10.1021/acssynbio.0c00039] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crocins are highly valuable medicinal compounds for treating human disorders, and they also serve as spices and coloring agents. However, the supply of crocins from plant extractions is insufficient for current demands, and using synthetic biology to produce crocins remains a big challenge. Here, we report the in vivo production of five types of crocins in E. coli with GjUGT94E13 and GjUGT74F8, which are responsible for the glycosylation of crocetin, from the crocin-producing plant Gardenia jasminoides. Subsequently, native UDP-glucose biosynthesis in E. coli is strengthened by the overexpression of pgm and galU. The optimization of catalytic reactions has demonstrated that 50 mM NaH2PO4-Na2HPO4 buffer (pH 8.0) plus 5% glucose is the best medium to use for the efficient glycosylation of crocetin. In engineered E. coli, the conversion rate of crocin III and crocin V from crocetin (50 mg/L) by the catalysis of GjUGT74F8 was increased to 66.1%, and the conversion rate of five types of crocins from crocetin (50 mg/L) via GjUGT94E13 and GjUGT74F8 was 59.6%, much higher than the catalytic activity of the reported microbial UGTs. This study not only sheds light on the in vivo biosynthesis of crocins in E. coli, but also provides important genetic tools for the de novo synthesis of crocins.
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Affiliation(s)
- Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Chunnian He
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Yan Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Wei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Kaizhi Hu
- Chongqing Institute of Medicinal Plant Cultivation, Chongqing, 408435, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, 666100, China
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27
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Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Crocin Biosynthesis in Gardenia jasminoides Ellis (Rubiaceae). BIOMED RESEARCH INTERNATIONAL 2020; 2020:2903861. [PMID: 32337236 PMCID: PMC7165322 DOI: 10.1155/2020/2903861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/29/2020] [Accepted: 03/12/2020] [Indexed: 11/17/2022]
Abstract
Crocins, enriched in Gardenia jasminoides fruits, have a pharmacological activity against central nervous system diseases, cardiovascular diseases, and cancer cell growth. The biosynthesis of crocins has been widely explored, but its regulatory mechanism remains unknown. Here, the basic helix-loop-helix (bHLH) transcription factors related to crocin biosynthesis were systematically identified on the basis of the genome of G. jasminoides. A total of 95 GjbHLH transcription factor genes were identified, and their phylogenetic analysis indicated that they could be classified into 23 subfamilies. The combination of gene-specific bHLH expression patterns, the coexpression analysis of biosynthesis genes, and the analysis of promoter sequences in crocin biosynthesis pathways suggested that nine bHLHs in G. jasminoides might negatively regulate crocin biosynthesis. This study laid a foundation for understanding the regulatory mechanism of crocin biosynthesis and the improvement and breeding of G. jasminoides varieties.
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Wu SH, Li HB, Li GL, Lv N, Qi YJ. Metabolite identification of gut microflora-cassia seed interactions using UPLC-QTOF/MS. Exp Ther Med 2020; 19:3305-3315. [PMID: 32266027 PMCID: PMC7132226 DOI: 10.3892/etm.2020.8585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Cassia seed is the dried ripe seed of Cassia obtusifolia L. or Cassia tora L., which is widely used as a food or traditional Chinese medicine. The aim of the present study was to detect the components and metabolites in the culture of human or rat intestinal microflora suspension with the water decoction of cassia seed in vitro, using an ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry system equipped with a negative ion scan mode. Initially, ellagic acid was identified in the cassia seed decoction. Subsequently, six different metabolites, including urolithin (uro)-A, uro-B, uro-D, uro-M6, uro-M7 and uro-B-glucuronide (glur), were detected after co-culture of the cassia seed decoction with intestinal microflora, but not in the cassia seed decoction alone. Uro-M6, uro-M7, uro-A and uro-B were common metabolites in the culture of human or rat intestinal microflora suspension with the water decoction of cassia seed. However, uro-D was only detected in the culture of rat intestinal microflora suspension with the water decoction of cassia seed, and uro-B-glur was only detected in the culture of human intestinal microflora with the water decoction of cassia seed. The uro and intermediate metabolites were produced by ellagic acid in the cassia seed decoction under the action of the intestinal microflora. The production of metabolites might be related to the abundance and diversity of the intestinal microflora in humans and rats. The present study provided rationale for further pharmacological and clinical studies on the mechanisms of action of cassia seeds.
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Affiliation(s)
- Su-Hui Wu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P.R. China
| | - Han-Bing Li
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P.R. China
| | - Gen-Lin Li
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P.R. China
| | - Ning Lv
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P.R. China
| | - Yue-Juan Qi
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P.R. China
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Gao RR, Hu YT, Dan Y, Hao LJ, Liu X, Song JY. Chinese herbal medicine resources: Where we stand. CHINESE HERBAL MEDICINES 2020; 12:3-13. [PMID: 36117557 PMCID: PMC9476789 DOI: 10.1016/j.chmed.2019.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/19/2019] [Accepted: 08/23/2019] [Indexed: 01/20/2023] Open
Abstract
In recent years, the development of Chinese herbal medicine (CHM) has been challenged by shortages of CHM resources and drug safety concerns related to end products. There have been significant efforts by Chinese scholars to tackle these challenges, which are revealed by analyzing the research trend of CHM resources via surveying Chinese Traditional and Herbal Drugs (Zhong Cao Yao), a representative journal in CHM. Our study focused on 781 articles in CHM resources from 2013 to 2018 and included four subject areas: germplasm resources, quality analysis and evaluation, cultivation, and bioengineering of CHM. Discussion and prospective for future investigations were also presented, including: construct the core germplasm of medicinal plants and expand germplasms; combine molecular research with field experiments and promote the deeper study of cultivation of CHM plants; improve the quality evaluation method of CHM and strengthen the identification of Chinese patented medicines; promote the sustainable development of CHM resources by utilizing bioengineering and synthetic biology. This study helps international scholars understand the status quo of CHM research and provides theoretical support for the healthy, modern, and international development of CHM, and it will facilitate the sustainable development of the traditional Chinese medicine industry.
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Li HK, Zhang WD, Gu Y, Wu GS. Strategy of systems biology for visualizing the “Black box” of traditional Chinese medicine. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2020. [DOI: 10.4103/wjtcm.wjtcm_31_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Cai P, Qiu H, Qi F, Zhang X. The toxicity and safety of traditional Chinese medicines: Please treat with rationality. Biosci Trends 2019; 13:367-373. [PMID: 31564696 DOI: 10.5582/bst.2019.01244] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Pingping Cai
- Department of Traditional Chinese Medicine, Shandong Provincial Hospital affiliated to Shandong Universityy, Ji'nan, China
| | - Hua Qiu
- Department of gynecology, Jinan Municipal Hospital of Traditional Chinese Medicine, Ji'nan, China
| | - Fanghua Qi
- Department of Traditional Chinese Medicine, Shandong Provincial Hospital affiliated to Shandong Universityy, Ji'nan, China
| | - Xiaoyi Zhang
- Department of Traditional Chinese Medicine, Shandong Provincial Hospital affiliated to Shandong Universityy, Ji'nan, China
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Dandara C, Masimirembwa C, Haffani YZ, Ogutu B, Mabuka J, Aklillu E, Bolaji O. African Pharmacogenomics Consortium: Consolidating pharmacogenomics knowledge, capacity development and translation in Africa: Consolidating pharmacogenomics knowledge, capacity development and translation in Africa. AAS Open Res 2019; 2:19. [PMID: 32382701 PMCID: PMC7194139 DOI: 10.12688/aasopenres.12965.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 12/22/2022] Open
Abstract
The African Pharmacogenomics Consortium (APC) was formally launched on the 6th September 2018. This white paper outlines its vision, and objectives towards addressing challenges of conducting and applying pharmacogenomics in Africa and identifies opportunities for advancement of individualized drugs use on the continent. Africa, especially south of the Sahara, is beset with a huge burden of infectious diseases with much co-morbidity whose multiplicity and intersection are major challenges in achieving the sustainable development goals (SDG), SDG3, on health and wellness. The profile of drugs commonly used in African populations lead to a different spectrum of adverse drug reactions (ADRs) when compared to other parts of the world. Coupled with the genetic diversity among Africans, the APC is established to promote pharmacogenomics research and its clinical implementation for safe and effective use of medicine in the continent. Variation in the way patients respond to treatment is mainly due to differences in activity of enzymes and transporters involved in pathways associated with each drug’s disposition. Knowledge of pharmacogenomics, therefore, helps in identifying genetic variants in these proteins and their functional effects. Africa needs to consolidate its pharmacogenomics expertise and technological platforms to bring pharmacogenomics to use.
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Affiliation(s)
- Collet Dandara
- Pathology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | | | - Yosr Z Haffani
- Higher Institute of Biotechnology Sidi Thabet, Manouba University, Ariana, LR17ES03, Tunisia
| | - Bernhards Ogutu
- Centre for Research in Therapeutic Sciences, Strathmore University, Nairobi, Kenya
| | - Jenniffer Mabuka
- Secretariat, The African Academy of Sciences (AAS), Nairobi, Kenya
| | - Eleni Aklillu
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Oluseye Bolaji
- Department of Pharmaceutical Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria
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Zhang Y, Ji A, Xu Z, Luo H, Song J. The AP2/ERF transcription factor SmERF128 positively regulates diterpenoid biosynthesis in Salvia miltiorrhiza. PLANT MOLECULAR BIOLOGY 2019; 100:83-93. [PMID: 30847712 DOI: 10.1007/s11103-019-00845-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 02/18/2019] [Indexed: 05/02/2023]
Abstract
The novel AP2/ERF transcription factor SmERF128 positively regulates diterpenoid tanshinone biosynthesis by activating the expression of SmCPS1, SmKSL1, and SmCYP76AH1 in Salvia miltiorrhiza. Certain members of the APETALA2/ethylene-responsive factor (AP2/ERF) family regulate plant secondary metabolism. Although it is clearly documented that AP2/ERF transcription factors (TFs) are involved in sesquiterpenoid biosynthesis, the regulation of diterpenoid biosynthesis by AP2/ERF TFs remains elusive. Here, we report that the novel AP2/ERF TF SmERF128 positively regulates diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza. Overexpression of SmERF128 increased the expression levels of copalyl diphosphate synthase 1 (SmCPS1), kaurene synthase-like 1 (SmKSL1) and cytochrome P450 monooxygenase 76AH1 (SmCYP76AH1), whereas their expression levels were decreased when SmERF128 was silenced. Accordingly, the content of tanshinone was reduced in SmERF128 RNA interference (RNAi) hairy roots and dramatically increased in SmERF128 overexpression hairy roots, as demonstrated through Ultra Performance Liquid Chromatography (UPLC) and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. Furthermore, SmERF128 activated the expression of SmCPS1, SmKSL1, and SmCYP76AH1 by binding to the GCC box, and to the CRTDREHVCBF2 (CBF2) and RAV1AAT (RAA) motifs within their promoters during in vivo and in vitro assays. Our findings not only reveal the molecular basis of how the AP2/ERF transcription factor SmERF128 regulates diterpenoid biosynthesis, but also provide useful information for improving tanshinone production through genetic engineering.
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Affiliation(s)
- Yu Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- College of Chinese Materia Medica, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
| | - Aijia Ji
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Hongmei Luo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, 666100, China.
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China.
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Ji C, Kriaucionis S, Kessler BM, Jiang C. From herbal small RNAs to one medicine. SCIENCE CHINA-LIFE SCIENCES 2019; 62:285-287. [PMID: 30863963 PMCID: PMC7089335 DOI: 10.1007/s11427-019-9513-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Chao Ji
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Pharmacology, Peking Union Medical College, Beijing, 100005, China
| | | | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, CAMS-Oxford Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Chengyu Jiang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS-Oxford Institute, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China.
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35
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Zhang Y, Zheng L, Zheng Y, Zhou C, Huang P, Xiao X, Zhao Y, Hao X, Hu Z, Chen Q, Li H, Wang X, Fukushima K, Wang G, Li C. Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum. FRONTIERS IN PLANT SCIENCE 2019; 10:1274. [PMID: 31681373 PMCID: PMC6813658 DOI: 10.3389/fpls.2019.01274] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 09/12/2019] [Indexed: 05/05/2023]
Abstract
Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue, and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.
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Affiliation(s)
- Yonghong Zhang
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Lanlan Zheng
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Yan Zheng
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Ping Huang
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Xiao Xiao
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Yongheng Zhao
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Xincai Hao
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Zhubing Hu
- Center for Multi-Omics Research Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qinhua Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, China
| | - Hongliang Li
- Laboratory of Chinese Herbal Pharmacology, Oncology Center, Renmin Hospital, Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
| | - Xuanbin Wang
- Laboratory of Chinese Herbal Pharmacology, Oncology Center, Renmin Hospital, Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Guodong Wang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, Ministry of Education, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Chen Li
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
- *Correspondence: Guodong Wang, ; Chen Li,
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